MolNFT v1 · #162312 · protein
Crystal structure of ppep-1(E184A)
6R54 · Pro-pro endopeptidase: “Crystal structure of ppep-1(E184A)”. X-ray diffraction, 2 ligands (ZN, NI), 3 pockets (best druggability 0.73). MolNFT v1 #162312 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6R54
- Type
- protein
- Length
- 393 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pro-pro endopeptidase
- EC
- 3.4.24.89
- UniProt
- Q183R7
- Ligands
- ZN, NI
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pro-pro endopeptidase (EC 3.4.24.89) | protein | 198 | 54% helix, 8% strand | Q183R7 |
| B | Pro-pro endopeptidase (EC 3.4.24.89) | protein | 195 | 53% helix, 8% strand | Q183R7 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 817 | 0.73 | 0.78 | 75 | TRS, ZN |
| 2 | 266 | 0.57 | 0.77 | 28 | TRS, ZN |
| 3 | 53 | 0.23 | 0.72 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 448 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q183R7
- Elsewhere: RCSB PDB 6R54 · PDBe 6R54 · UniProt Q183R7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.